To develop a systems biology model of fibrosis progression within the human lung we performed RNA sequencing and microRNA analysis on 95 samples obtained from 10 idiopathic pulmonary fibrosis (IPF) and 6 control lungs. Extent of fibrosis in each sample was assessed by microCT-measured alveolar surface density (ASD) and confirmed by histology. Regulatory gene expression networks were identified using linear mixed-effect models and dynamic regulatory events miner (DREM). Differential gene expression analysis identified a core set of genes increased or decreased before fibrosis was histologically evident that continued to change with advanced fibrosis. DREM generated a systems biology model (www.sb.cs.cmu.edu/IPFReg) that identified progressively divergent gene expression tracks with microRNAs and transcription factors that specifically regulate mild or advanced fibrosis. We confirmed model predictions by demonstrating that expression of POU2AF1, previously unassociated with lung fibrosis but proposed by the model as regulator, is increased in B lymphocytes in IPF lungs and that POU2AF1-knockout mice were protected from bleomycin-induced lung fibrosis. Our results reveal distinct regulation of gene expression changes in IPF tissue that remained structurally normal compared with moderate or advanced fibrosis and suggest distinct regulatory mechanisms for each stage.

To detect Zika virus more rapidly and accurately, we developed a novel method that utilized a real-time fluorescence reverse transcription loop-mediated isothermal amplification (LAMP) technique. The NS5 gene was amplified by a set of six specific primers that recognized six distinct sequences. The amplification process, including 60 min of thermostatic reaction with Bst DNA polymerase following real-time fluorescence reverse transcriptase using genomic Zika virus standard strain (MR766), was conducted through fluorescent signaling. Among the six pairs of primers that we designate here, NS5 was the most efficient with a high sensitivity of up to 3.3 ng/μl and reproducible specificity on eight pathogen samples that were used as negative controls. The real-time fluorescence reverse transcription LAMP detection process can be completed within 35 min. Our study demonstrated that real-time fluorescence reverse transcription LAMP could be highly beneficial and convenient clinical application to detect Zika virus due to its high specificity and stability.

To explore underlying mechanism of urinary stones formation, the composition and microstructure of urinary stones were analyzed systematically with a large sample study from China. A total of 2437 urinary stones were obtained from the urology department at our Hospital. The composition of the stones was analyzed by Fourier transform infrared spectroscopy (FTIR). Meanwhile, the microstructure and element distribution were observed with scanning electron microscopy combined with element distribution analysis (SEM-EDAX). Urinary stones were classified into eight types, that were consisted of calcium oxalate stones (1301/2437, 53.39%), calcium phosphate stones (131/2437, 5.38%), anhydrous uric acid stones (434/2437, 17.81%), magnesium ammonium phosphate stones (12/2437, 0.49%), sodium urate stones (5/2437, 0.21%), brushite stones (4/2437, 0.16%), cystine stones (3/2437, 0.12%) and mixed stones (547/2437, 22.45%, ten subtypes were included). Under SEM, they displayed distinct microstructures: plank-like, brick-like, polyhedron or paliform crystals for calcium oxalate stones, similar sized echin-sphere or rough bulbiform or tree bark-like crystals for calcium phosphate stones, rotten-wood-like or petrous crystals for anhydrous uric acid stones, globular or gallet-like crystals for magnesium ammonium phosphate stones, sawdust-like crystals for sodium urate stones, broken-wood-like crystals for brushite stones, stacking hexagonal cystine crystals for cystine stones, and two or more of the above crystals for mixed stones. Meanwhile, they also presented distinct elemental composition and distribution by EDAX. Urinary stones can be classified into eight types, and exhibit a diversity of microstructure and elemental compositions in China. The formation process of different types of urinary stones may be diverse.

To provide some basis for the prevention of urinary stones in general population, we did a systemic analysis of urinary stones from Northern, Eastern, Central, Southern and Southwest China by a multi-center study. A total of 11,157 urinary stones from Northern, Eastern, Central, Southern and Southwest China were obtained and analyzed by Fourier transform infrared spectroscopy. Combined with scanning electron microscopy and X-ray energy spectrometer, urinary stones were classified into different types. Furthermore, the correlation between stone types and clinical characteristics, as well as their regional distribution were elucidated. Calcium oxalate stones were the most common type in each region, followed by calcium oxalate-calcium phosphate mixed stones, uric acid stones and calcium phosphate stones. The distribution of calcium oxalate stones were highest prevalence in Southwest China (67.9%, P < 0.05), followed by Eastern and Northern China. Anhydrous uric acid stones, with a constituent ratio of 19.3% in Southern China, and 13.7% in Central China, were significantly higher than that in other regions (P < 0.05). Elements analysis indicated varieties among stone types as well as distribution regions. Moreover, the clinical characteristics were highly correlated with stone types and anatomical locations but not their distribution regions. The material and elements composition of urinary stones among different regions showed some varieties. Calcium oxalate stone has the highest constituent ratio in Southwest China, while anhydrous uric acid stone has the highest constituent ratio in Southern China. Moreover, the clinical characteristics were highly correlated with stone types and anatomical locations but not their distribution regions.

Limited studies have been conducted on calcium phosphate gallbladder stones, to enhance our comprehension of the formation, we investigated the clinical characteristics and the potential link between calcium phosphate gallbladder stones and Clonorchis sinensis (C sinensis ) infection. A retrospective observational study was conducted involving 4451 patients who underwent gallbladder-preserving cholelithotomy between January 2013 and January 2022. Based on the regional prevalence of C sinensis infection, the patients were categorized into 2 groups: those from high-incidence regions and those from low-incidence regions. We analyzed their appearance, texture, and clinical attributes. Furthermore, we utilized light microscopy to detect C sinensis eggs and χ ² tests to analyze the detection rate. Additionally, Fourier transform infrared spectroscopy was employed to analyze stone composition, and scanning electron microscopy combined with element distribution analysis (SEM-EDAX) was used to observe microstructure and element distribution. A total of 245 cases were identified as calcium phosphate stones, which constituted 5.50% (245/4451) of all gallbladder stone cases. These stones exhibited various degrees of bilirubinate mixing, with nearly 19.18% (47/245) being combined with calcium carbonate (CaCO3). The presence of C sinensis eggs in calcium phosphate stones was significantly higher compared to non-calcium phosphate–CaCO ₃ –bilirubinate stones ( P < .05). Moreover, the prevalence of calcium phosphate stones was notably greater in C sinensis high-incidence regions than in low-incidence regions ( P < .05). Calcium phosphate stones represent a significant subset of gallbladder stones. They frequently occur in combination with bilirubinate in varying proportions, and less commonly with other components. The development of calcium phosphate stones was associated with C sinensis infection. Therefore, effective prevention of this parasitic infection is essential for reducing the risk of calcium phosphate stone formation.

Lung adenocarcinoma (LUAD) is one of the most common causes of cancer-related death. The role of pyroptosis in LUAD remains unclear. Our study aimed to identify a prognostic signature of pyroptosis-related genes (PRGs) and explore the connection of PRGs with the tumour microenvironment in LUAD. Gene expression and clinical information were obtained from The Cancer Genome Atlas database. Consensus clustering was applied to classify LUAD patients. The least absolute shrinkage and selection operator Cox and multivariate Cox regression models were used to generate a PRG-related prognostic signature. The correlations between PRGs and tumour-infiltrating immune cells or the tumour mutational burden were analysed by Spearman’s correlation analysis. In this study, 44 PRGs significantly differed in expression between LUAD and normal tissues. Based on these genes, patients were clustered into three clusters with significantly different distributions of tumour-infiltrating immune cells and immune checkpoint regulators. A total of four PRGs (NLRP1, HMGB1, CYCS, and BAK1) were used to construct a prognostic model. Significant correlations were observed between these prognostic PRGs and immune cell infiltration or the tumour mutational burden. Predictive nomogram results showed that BAK1 could be an independent prognostic biomarker in LUAD. Additionally, the expression level of BAK1 was validated in two independent Gene Expression Omnibus cohorts. Our identified prognostic PRG signature may provide insight for future studies targeting pyroptosis and the tumour microenvironment in LUAD. Future studies are needed to verify our current findings.